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[Rp] Reproducibility of 'Poincaré Dodecahedral Space Parameter RESCIENCE C Reproduction / Astronomy [¬Rp] Reproducibility of ’Poincaré dodecahedral space parameter estimates’ Boudewijn F. Roukema1,2, ID 1Institute of Astronomy, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Toruń, Poland – 2Univ Lyon, Ens de Lyon, Univ Lyon1, CNRS, Centre de Recherche Astrophysique de Lyon UMR5574, F–69007, Lyon, France Edited by Pierre de Buyl ID Abstract Reviewed by Is a scientific research paper based on (i) public, online observational data files Konrad Hinsen ID and (ii) providing free-licensed soware for reproducing its results easy to reproduce by the same author a decade later? This paper attempts to reproduce a cosmic topol- Received ogy observational paper published in 2008 and satisfying both criteria (i) and (ii). 05 May 2020 The reproduction steps are defined formally in a free-licensed git repository pack- age “0807.4260” and qualitatively in the current paper. It was found that the effort in Published 14 July 2020 upgrading the Fortran 77 code at the heart of the soware, interfaced with a C front end, and originally compiled with g77, in the content of the contemporary gfortran DOI compiler, risked being too great to be justified on any short time scale. In this sense, 10.5281/zenodo.3956058 the results of RBG08 are not as reproducible as they appeared to be, despite both (i) data availability and (ii) free-licensing and public availability of the soware. The soware and a script to reproduce the steps of this incomplete reproduction are com- bined in a new git repository named 0807.4260, following the ArXiv identity code of RBG08. [23] 1 Introduction This paper studies the reproducibility of the main observational results of a cosmic topology research paper published by myself and co-authors in 2008[23]. The paper used the surface-of-last-scattering optimal cross-correlation method of finding a pre- ferred orientation of the fundamental domain of the spatial section of the Universe, under the working hypothesis that the spatial section is a Poincaré dodecahedral space[17]. The code was developed by me, with comments provided by my coau- thors. The results that should be reproduced are those that use the method described in Section 3.2 of RBG08, and the observational analysis results described in Section 4.2, displayed in Figs. 3, 4, 5 and given numerically in Tables 2 and 3 of RBG08. Re- lated cosmic topology papers by other authors are published with no references to arXiv:2008.07380v1 [cs.CY] 23 Jul 2020 soware package details or soware licences. The reason for attempting and documenting the reproducibility of this paper is that not only are many papers in astronomy[3] and other fields still published without providing the full empirical data sets and source code under free-soware licences, but even those that provide free-licensed soware and input data may be difficult to reproduce[14, 7, 25]. While observational data in cosmology are usually made avail- able online with high-quality documentation, oen aer an embargo period, free- licensed soware in the field of cosmic topology, in particular, library functions for Copyright © 2020 B.F. Roukema, released under a Creative Commons Attribution 4.0 International license. Correspondence should be addressed to Boudewijn F. Roukema (boud astro.uni.torun.pl) The authors have declared that no competing interests exist. Code is available at https://codeberg.org/boud/0807.4260. –SWH swh:1:dir:4f1fe8cf5a01bb4637e31ea938eaa5bc25a2b87b. Data is available at https://lambda.gsfc.nasa.gov/data/map/dr3/dfp/wmap_ilc_5yr_v3.fits. Open peer review is available at https://github.com/ReScience/submissions/issues/41. ReScience C 6.1 (#11) – Roukema 2020 1 [¬Rp] Reproducibility of ’Poincaré dodecahedral space parameter estimates’ defining matched circles in the cosmic microwave background or matched discs in extragalactic 3-dimensional comoving space[21], is only recorded in the scientific lit- erature in papers published by my research group. To document and help analyse the success and difficulties in reproducing scien- tific results in this context, the editors of ReScience C posed the “Ten Years Repro- ducibility Challenge”, a request that scientists attempt to reproduce the main results of their own peer-reviewed scientific research papers that had been published before 1 January 2010, and document the method and results in ReScience C[18]. 2 Method The first steps for trying to reproduce the original results of RBG08 were to (re-)read the appropriate sections of the paper, initially taking the view of a non-author. 1. Section 2.1[23] states that the analysis method of Section 3.2 requires the three files at URLs listed in footnotes 1, 2, 3 on the same page. These files repre- sent two versions of an all-sky map of the Universe mostly representing cosmic −1 microwave background emission at 10h Gpc (comoving) from the Earth as observed by the Wilkinson Microwave Anisotropy Probe (WMAP)[11], and the “kp2” mask to enable analysis that avoids the most contaminated regions of the sky. These files need to be downloaded. 2. Footnote 7[23] indicates that circles-0.3.2.1, to be found at the URL http://cosmo. torun.pl/GPLdownload/dodec/, provides the soware for generating the figures and tables. This soware needs to downloaded from http://cosmo.torun.pl/GPLdownload/ dodec/circles-0.3.2.1.tar.gz. The next step was to develop a script on a git repository server that satisfies the re- quirements of the international scientific community, specifically the International Science Council[13], by not blocking access to scientists of any countries or territo- ries. During 2018 and 2019, several of the most popular git repository servers partially blocked access to scientists and other residents of several countries and territories (Github[10, 16, 26], Bitbucket[15], Gitlab[24]; the gitlab soware is free-licensed and can be installed independently of the Gitlab online service). The bans have presum- ably continued into 2020. A shi of my own soware to servers acceptable under in- ternational scientific ethical standards is underway, but incomplete as of early 2020. I chose a community-based server, Codeberg, not currently listed on the Wikipedia list of source code hosting facilities1. In 2019, the Investigating & Archiving the Scholarly Git Experience project team expressed its concerns about the bans, describing them as having “far-reaching and chilling consequences for open source, open scholarship, and for the open exchange of information and ideas”[12]. The remaining planned steps were to implement the minimal number of updates to make the code work and replicate the original results, using modern hardware and a modern soware environment. Footnote 7 of RBG08 warns that “These [circles- 0.3.2.1 and circles-0.3.8] and earlier versions of the soware require medium to ad- vanced GNU/Linux, Fortran77 and C experience for a scientific user.” There is no statement regarding the particular compiler(s) used. As far as I recall, it’s very likely that the widely used GNU fortran compiler of the time, g77, was used together with gcc, as selected automatically by autotool packages. The system and hardware chosen for the reproduction project were an AMD com- puter running with a Debian GNU/Linux 9.12 system on an x86_64 Linux-4.9.0 ker- nel. The Fortran compiler chosen was GNU Fortran (Debian 6.3.0-18+deb9u1) 6.3.0 20170516. 3 Results The overall script intended to carry out the full sequence of downloads, configuring of packages, compiling of packages, subdirectory user-level installation of packages, 1https://en.wikipedia.org/wiki/Comparison_of_source-code-hosting_facilities ReScience C 6.1 (#11) – Roukema 2020 2 [¬Rp] Reproducibility of ’Poincaré dodecahedral space parameter estimates’ ded213c1c4cfdfe2ef92f7155b27d58c wmap_ilc_5yr_v3.fits fbc8b2518fdddf0a1e7b5acde99a748e wiener5yr_map.fits 5aa3267dc6d69bf8c5f0a3a893e23960 wmap_kp2_r9_mask_3yr_v2.fits afbd67d8120c11e949eb0c414c2775f5 circles-0.3.2.1.tar.gz Table 1. Checksums (md5sums) of the data and the main soware source code files of RBG08, use for the present reproducibility test. setting up of calculation parameters, and running the main code, was set up as a bash script reproduce_RBG08.sh. The full package aiming to reproduce the figures and tables listed above is pro- vided at https://codeberg.org/boud/0807.4260, named aer the ArXiv identity of RBG08. 3.1 Downloading data and software source code 1. The URL in footnotes 1, 2 and 3[23] gave clickable links that were split into two and not correctly clickable. The user needs to cut/paste the two halves of each URL in order to obtain the three data files. The data files were downloaded with no apparent problem, with md5sums as indicated in Table 1. 2. The file circles-0.3.2.1.tar.gz with the md5sum indicated in Table 1 was down- loaded. It was included in the main git repository in its original form. Subse- quent changes are recorded in the git history at https://codeberg.org/boud/0807. 4260. 3.2 Compiling/debugging Fixes needed in order to successfully compile circles include: 1. A Fortran 77 line that ended on one line with a + symbol and started on the next line with another + symbol (within the valid columns for standard Fortran 77) was apparently accepted by the gcc family fortran compiler in 2008, but not now (2020). One of the + symbols was removed. 2. A fitting algorithm gsl_multifit_covar available in GNU Scientific Library (GSL) versions 1.x was obsoleted; it is no longer present in modern 2.x versions of GSL. With the aim of minimising the interventions required in the system, GSL- 1.10 was downloaded and compiled from source, re-creating part of the original soware environment. 3. Using the modern gfortran compiler options -fcheck=bounds -Wall to highlight likely sources of bugs due to insufficiently standard coding led to many warn- ings.
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